Combined Use of 2-D NMR Correlation Experiments, GIAO DFT 13C Chemical Shifts and 1-D NOESY Methods in Regioisomeric and Conformational Structure Determination of Cyclophanes in Solution

2011 ◽  
Vol 41 (2-4) ◽  
pp. 467-475 ◽  
Author(s):  
Shamil Latypov ◽  
Nataly Epifanova ◽  
Elena Popova ◽  
Sergey Vasilevsky ◽  
Svetlana Solovieva ◽  
...  
2008 ◽  
Vol 2008 (27) ◽  
pp. 4640-4646 ◽  
Author(s):  
Shamil Latypov ◽  
Alsu Balandina ◽  
Marco Boccalini ◽  
Alessandra Matteucci ◽  
Konstantin Usachev ◽  
...  

2021 ◽  
Vol 8 ◽  
Author(s):  
Kari Gaalswyk ◽  
Zhihong Liu ◽  
Hans J. Vogel ◽  
Justin L. MacCallum

Paramagnetic nuclear magnetic resonance (NMR) methods have emerged as powerful tools for structure determination of large, sparsely protonated proteins. However traditional applications face several challenges, including a need for large datasets to offset the sparsity of restraints, the difficulty in accounting for the conformational heterogeneity of the spin-label, and noisy experimental data. Here we propose an integrative approach to structure determination combining sparse paramagnetic NMR with physical modelling to infer approximate protein structural ensembles. We use calmodulin in complex with the smooth muscle myosin light chain kinase peptide as a model system. Despite acquiring data from samples labeled only at the backbone amide positions, we are able to produce an ensemble with an average RMSD of ∼2.8 Å from a reference X-ray crystal structure. Our approach requires only backbone chemical shifts and measurements of the paramagnetic relaxation enhancement and residual dipolar couplings that can be obtained from sparsely labeled samples.


2020 ◽  
Author(s):  
Jordana T. Brito ◽  
Lucas H. Martorano ◽  
Ana Carolina F. de Albuquerque ◽  
Carlos Magno Rocha Ribeiro ◽  
Rodolfo Goetze Fiorot ◽  
...  

In the past, structure determination of natural products was an arduous process depending almost entirely on chemical synthesis, mainly by derivatization and degradation processes, taking years of effort. Recently, structural elucidation of natural products has undergone a revolution. Nowadays, with the combined use of different advanced spectroscopic methods, it became possible to completely assign the structure of natural products using small amounts of sample. However, despite the extraordinary ongoing advances in spectroscopy, the mischaracterization of natural products has been and remains a recurrent problem, especially in the presence of several chiral centers. The misinterpretation of NMR data has resulted in frequent reports addressing the issue of structural reassignment. In this context, a great effort has been devoted to the development of quantum chemical calculations to predict NMR parameters, and thus achieve a more accurate spectral interpretation. In this work, we applied a protocol for theoretical calculations of 1H NMR chemical shifts in order to establish the correct and unequivocal structure of Helianuol L, a member of the Heliannuol’s class, isolated from Helianthus annus. These secondary metabolites present a broad spectrum of biological activities, including the allelochemical activity, making them promising candidates as natural agrochemicals. It is worth mentioning, however, that the process of elucidating the structure of Heliannuol L was based on structural correlations with molecules already known in the literature, where few stereochemical analyses were performed. In this way, based on the fact that other compounds of the Heliannuol’s class had their structure previously reassigned, the verification of the proposed structure of Heliannuol L becomes of great importance.


2019 ◽  
Vol 141 (42) ◽  
pp. 16624-16634 ◽  
Author(s):  
Albert Hofstetter ◽  
Martins Balodis ◽  
Federico M. Paruzzo ◽  
Cory M. Widdifield ◽  
Gabriele Stevanato ◽  
...  

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